001package org.biopax.paxtools.model.level3; 002 003 004/** 005 * Definition: The biological source of an entity (e.g. protein, RNA or DNA). Some entities are 006 * considered source-neutral (e.g. small molecules), and the biological source of others can be 007 * deduced from their constituentss (e.g. complex, pathway). Examples: HeLa cells, human, and mouse 008 * liver tissue. 009 */ 010public interface BioSource extends UtilityClass, Named 011{ 012 013 /** 014 * A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. 015 * Best practice is to refer to <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell">OBOCell 016 * Ontology</a>. 017 * @return cell type if this biosource is a cell line or a specific tissue. Null otherwise. 018 */ 019 CellVocabulary getCellType(); 020 021 /** 022 * A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. 023 * Best practice is to refer to <a href="http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell">OBOCell 024 * Ontology</a>. 025 * @param cellType if this biosource is a cell line or a specific tissue. Null for n/a. 026 */ 027 void setCellType(CellVocabulary cellType); 028 029 030 /** 031 * An external controlled vocabulary of tissue types. A reference to the 032 * <a href="http://www.brenda-enzymes.info/">BRENDA</a> 033 * @return An external controlled vocabulary of tissue types. 034 */ 035 TissueVocabulary getTissue(); 036 037 /** 038 * An external controlled vocabulary of tissue types. A reference to the 039 * <a href="http://www.brenda-enzymes.info/">BRENDA</a> 040 * @param tissue An external controlled vocabulary of tissue types. 041 */ 042 void setTissue(TissueVocabulary tissue); 043}